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comparison CVInspector.xml @ 0:3070d71e0e5c draft

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author bgruening
date Thu, 16 Apr 2015 08:37:04 -0400
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-1:000000000000 0:3070d71e0e5c
1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="CVInspector" name="CVInspector" version="2.0.0">
3 <description>A tool for visualization and validation of PSI mapping and CV files.</description>
4 <macros>
5 <token name="@EXECUTABLE@">CVInspector</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio"/>
9 <expand macro="requirements"/>
10 <command>CVInspector
11
12 -cv_files
13 #for token in $param_cv_files:
14 $token
15 #end for
16
17 #if $rep_param_cv_names:
18 -cv_names
19 #for token in $rep_param_cv_names:
20 #if " " in str(token):
21 "$token.param_cv_names"
22 #else
23 $token.param_cv_names
24 #end if
25 #end for
26 #end if
27 #if $param_mapping_file:
28 -mapping_file $param_mapping_file
29 #end if
30
31 #if $rep_param_ignore_cv:
32 -ignore_cv
33 #for token in $rep_param_ignore_cv:
34 #if " " in str(token):
35 "$token.param_ignore_cv"
36 #else
37 $token.param_ignore_cv
38 #end if
39 #end for
40 #end if
41 #if $param_html:
42 -html $param_html
43 #end if
44 -threads \${GALAXY_SLOTS:-24}
45 #if $adv_opts.adv_opts_selector=='advanced':
46 #if $adv_opts.param_force:
47 -force
48 #end if
49 #end if
50 </command>
51 <inputs>
52 <param name="param_cv_files" type="data" format="obo" multiple="true" optional="False" size="30" label="List of ontology files in OBO format" help="(-cv_files) ">
53 <sanitizer>
54 <valid initial="string.printable">
55 <remove value="'"/>
56 <remove value="&quot;"/>
57 </valid>
58 </sanitizer>
59 </param>
60 <repeat name="rep_param_cv_names" min="1" title="param_cv_names">
61 <param name="param_cv_names" type="text" size="30" label="List of identifiers (one for each ontology file)" help="(-cv_names) ">
62 <sanitizer>
63 <valid initial="string.printable">
64 <remove value="'"/>
65 <remove value="&quot;"/>
66 </valid>
67 </sanitizer>
68 </param>
69 </repeat>
70 <param name="param_mapping_file" type="data" format="xml" optional="True" label="Mapping file in CVMapping (XML) format" help="(-mapping_file) "/>
71 <repeat name="rep_param_ignore_cv" min="0" max="1" title="param_ignore_cv">
72 <param name="param_ignore_cv" type="text" size="30" value="UO PATO BTO" label="A list of CV identifiers which should be ignored" help="(-ignore_cv) ">
73 <sanitizer>
74 <valid initial="string.printable">
75 <remove value="'"/>
76 <remove value="&quot;"/>
77 </valid>
78 </sanitizer>
79 </param>
80 </repeat>
81 <expand macro="advanced_options">
82 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
83 </expand>
84 </inputs>
85 <outputs>
86 <data name="param_html" format="html"/>
87 </outputs>
88 <help>**What it does**
89
90 A tool for visualization and validation of PSI mapping and CV files.
91
92
93 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_CVInspector.html</help>
94 <expand macro="references"/>
95 </tool>